I have seen several breakdown and rough rules for adjusting a monster's CR according to various special abilities and qualities. The Pathfinder Core book and Bestiary has rules about things like high and low damage, ability scores, and the bones of the process, but I am looking for more information about things like;

Incorporeal

Damage Reduction

Breath Weapons

Spell like abilities & caster level

Weaknesses like vulnerability to fire

Special Attacks

Constrict

Fly, swim, and burrow speeds

I have a solid understanding of what challenges this represent, and mostly adjust a monster's CR by ear, but I know I've seen several rough and ready rules for this.

Coming from a 3.5 perspective, my answer for you is that there's no solid answer. But, that isn't to say an answer can't be found. It's just not as specific as you're asking.

A monsters CR is the summary of all of its abilities. If I improve a grick's DR by one, it will have little to no effect on the entire encounter. But if I improve it by more while improving it's strength and say give it fast healing, then we have a substantially more difficult monster. There's just too many variables in play to base CR off of one or a few.

The 3.5 advanced monster CR rules are quite linear and easy to follow step-by-step. I have played CR by ear also, though unsuccessfully at times. It's best to do the math first, and don't forget to playtest. This is actually why I am looking for somewhere to playtest. All the math and estimation can only do so well, but ultimately one won't know how much of a threat that huge megaraptor poses until they put it up against whatever they plan on using it against in their game (ideally, as close to the projected team as possible).

It just depends too much on the monster itself, its tactics in combat, and the other abilities it already possesses. Even DR 10/- is much more useful to a mindflayer than it is to a bee.